# HG changeset patch
# User Ira Cooke <iracooke@gmail.com>
# Date 1370783858 18000
# Node ID 327b2d99d4c5f7586a1427a7812bfbd906ba6ab8
# Parent  d9564913a944bc4158eecfe43d8d0b7dc436a4ed
Update

diff -r d9564913a944 -r 327b2d99d4c5 README
--- a/README	Tue Mar 05 00:18:41 2013 -0500
+++ b/README	Sun Jun 09 08:17:38 2013 -0500
@@ -1,8 +1,10 @@
-This package installs wrapper scripts for running Mascot MS/MS searches
+This includes tools for running Mascot MS/MS searches
 
 Running this tool requires a working installation of Mascot (commercial software).
 Mascot is available from http://www.matrixscience.com/
 
 Requirements:
 This package depends on the galaxy_protk and protk_trans_proteomic_pipeline packages
-Please see instructions for those packages before installing
+Please see instructions for those packages before installing. In particular 
+you will need to install system package requirements for galaxy_protk and protk_trans_proteomic_pipeline
+using your package manager
diff -r d9564913a944 -r 327b2d99d4c5 mascot.xml
--- a/mascot.xml	Tue Mar 05 00:18:41 2013 -0500
+++ b/mascot.xml	Sun Jun 09 08:17:38 2013 -0500
@@ -2,13 +2,28 @@
 
 
 	<requirements>
-	    <requirement type="package" version="1.2.0">galaxy_protk</requirement>
+	    <requirement type="package" version="1.2.2">galaxy_protk</requirement>
    </requirements>
 
 	<description>Mascot MS/MS Search</description>
 
 
-	<command>rvm 1.9.3@protk-1.2.0 do mascot_search.rb -d $database -f $fragment_ion_tol -S $server $input_file -o $output -r
+	<command>rvm 1.9.3@protk-1.2.2 do mascot_search.rb 
+
+		#if $database.source_select=="built_in":
+		-d $database.dbkey
+		#else 
+		-d $database.custom_db
+		#end if
+
+		-f $fragment_ion_tol 
+
+		-S $server $input_file 
+
+		-o $output 
+
+		-r
+		
 		## Variable Mods
 
 		--var-mods='
@@ -18,34 +33,61 @@
 		--fix-mods='
 		$fixed_mods
 		'		
-		--allowed-charges=$allowed_charges	--enzyme=$enzyme --instrument=$instrument --precursor-ion-tol-units=$precursor_tolu --email=$email --username=$username -v $missed_cleavages
-		
+		--allowed-charges=$allowed_charges	
+
+		--enzyme=$enzyme 
+
+		--instrument=$instrument 
+
+		--precursor-ion-tol-units=$precursor_tolu 
+
+		--email=$email 
+
+		-v $missed_cleavages
+
+		#if $security.security_use
+		--use-security
+		--username $security.username
+		--password $security.password
+		#end if
+
+		#if $proxy
+		--proxy $proxy
+		#end if
+
 	</command>
 
 	<inputs>
 	
     <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/>
 
-	<param name="database" type="select" format="text" >
-	    <label>Database</label>
-		<options from_file="mascot_databases.loc">
-			<column name="name" index="0" />
-			<column name="value" index="2" />
-		</options>
-	</param>
+	<conditional name="database">
+		<param name="source_select" type="select" label="Database Type">
+			<option value="built_in">Built-In</option>
+			<option value="custom_defined">Custom</option>
+		</param>
+		<when value="built_in">
+			<param name="dbkey" type="select" format="text" >
+				<label>Database</label>
+				<options from_file="mascot_databases.loc">
+					<column name="name" index="0" />
+					<column name="value" index="2" />
+				</options>
+			</param>
+		</when>
+		<when value="custom_defined">
+			<param name="custom_db" type="text" size="80" value="SwissProt" label="Database Name" help="Exact name of a database defined on the Mascot server (case-sensitive)"/>
+		</when>
+	</conditional>
 
-
-
-	<param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
-		clicking to select multiple items">
+	<param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple values allowed">
 		<options from_file="mascot_mods.loc">
 			<column name="name" index="0" />
 			<column name="value" index="2" />
 		</options>
 	</param>		
 
-	<param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
-	clicking to select multiple items">
+	<param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple values allowed">
 		<options from_file="mascot_mods.loc">
 			<column name="name" index="0" />
 			<column name="value" index="2" />
@@ -108,24 +150,33 @@
 		<option value="CID+ETD">CID+ETD</option>
 	</param>
 	
-	<param name="fragment_ion_tol" label="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" help="Fragment ion tolerance in Daltons"/>
+	<param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.65" min="0" max="10000" help="Fragment ion tolerance in Daltons"/>
 
-	<param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" help="Precursor ion tolerance"/>
+	<param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" help="Enter a value in Daltons or ppm depending on the units chosen below"/>
 	<param name="precursor_tolu" type="select" format="text">
 	    <label>Precursor Ion Tolerance Units</label>
 	    <option value="ppm">ppm</option>		
 		<option value="Da">Da</option>
 	</param>
 
-	<param name="server" type="text" label="URL to Mascot Server cgi " size="60" value="http://www.exampleserver.com/mascot/cgi/"/>
+	<param name="server" type="text" label="URL to the cgi directory on the Mascot Server " size="60" value="http://www.exampleserver.com/mascot/cgi/"/>
+	<param name="proxy" type="text" label="Proxy Server URL including proxy port" size="60" value="" help="eg http://proxy.latrobe.edu.au:8080"/>
+
+	<conditional name="security">
+		<param name="security_use" type="boolean" label="Use Mascot Security?" help="Select this if you need to enter a username and password" truevalue="true" falsevalue="false" />
+		<when value="false" />
+		<when value="true">
+			<param name="username" type="text" label="Username" size="60" value="" help="Username on Mascot Server"/>
+			<param name="password" type="text" label="Password" size="60" value="" help="Mascot Password. Password is encrypted when over the internet but is stored in clear-text on the Galaxy server"/>
+		</when>
+	</conditional>
+	<param name="email" type="text" label="Email " size="60" value="" help=""/>
 	
-	<param name="email" type="text" label="Email " size="60" value="" help="Not Supported Yet."/>
 	
-	<param name="username" type="text" label="Username" size="60" value="" help="Not Supported Yet."/>	
 
   </inputs>
   <outputs>
-    <data format="mascotdat" name="output" metadata_source="input_file" label="mascot_vs_${database}.${input_file.display_name}.mascotdat"/>
+    <data format="mascotdat" name="output" metadata_source="input_file" label="mascot_vs_${database.dbkey if $database.has_key('dbkey') else $database.custom_db}.${input_file.display_name}.mascotdat"/>
   </outputs>
 
   <help>
diff -r d9564913a944 -r 327b2d99d4c5 mascot_to_pepxml.xml
--- a/mascot_to_pepxml.xml	Tue Mar 05 00:18:41 2013 -0500
+++ b/mascot_to_pepxml.xml	Sun Jun 09 08:17:38 2013 -0500
@@ -1,29 +1,80 @@
 <tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.0.1">
 	<requirements>
-	    <requirement type="package" version="1.2.0">galaxy_protk</requirement>
+	    <requirement type="package" version="1.2.2">galaxy_protk</requirement>
 	    <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
    </requirements>
 
   <description>Converts a mascot results file to pepXML</description>
 
-<command>rvm 1.9.3@protk-1.2.0 do mascot_to_pepxml.rb $input_file -o $output -d $database</command>
+<command>rvm 1.9.3@protk-1.2.2 do mascot_to_pepxml.rb 
+	$input_file 
+
+	-o $output 
+
+	#if $database.source_select=="built_in":
+	-d $database.dbkey
+	#else 
+	-d $database.fasta_file
+	#end if
+
+	#if $explicit_enzyme.explicit_enzyme_use
+	--enzyme $explicit_enzyme.enzyme
+	#end if
+
+	$shortid
+
+</command>
 <inputs>
 
+
 	<param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/>
-	<param name="database" type="select" format="text" >
-	    <label>Database</label>
-		<options from_file="pepxml_databases.loc">
-			<column name="name" index="0" />
-			<column name="value" index="2" />
-		</options>
-	</param>
-	
+
+	<conditional name="database">
+		<param name="source_select" type="select" label="Database source" help="A local copy of the database used in the Mascot search">
+			<option value="built_in">Built-In</option>
+			<option value="input_ref">Uploaded fasta file</option>
+		</param>
+		<when value="built_in">
+			<param name="dbkey" type="select" format="text" >
+				<label>Database</label>
+				<options from_file="pepxml_databases.loc">
+					<column name="name" index="0" />
+					<column name="value" index="2" />
+				</options>
+			</param>
+		</when>
+		<when value="input_ref">
+			<param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
+		</when>
+	</conditional>
+
+	<param name="shortid" type="boolean" label="Short ID" help="Use protein id from the Mascot result file instead reading from the fasta database." truevalue="--shortid" falsevalue="" />
+
+	<conditional name="explicit_enzyme">
+		<param name="explicit_enzyme_use" type="boolean" label="Specify Enzyme" help="If left unchecked the Enzyme will be read from the input file" truevalue="true" falsevalue="false" />
+		<when value="false" />
+		<when value="true">
+			<param name="enzyme" type="text" label="Enzyme" size="80" value="trypsin" help="Semi-cleavage can be specified as semisample_enyzme eg semitrypsin"/>
+		</when>
+	</conditional>
+
+
 
 </inputs>
 <outputs>
 	<data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
 </outputs>
 
+	<tests>
+    	<test>
+    		<param name="source_select" value="input_ref"/>
+	      	<param name="fasta_file" value="bsa.fasta"/>
+   		   	<param name="input_file" value="F002832.dat"/>
+      		<output name="output" file="bsa_mascot2xml.pep.xml" compare="sim_size" delta="600" /> 
+    	</test>
+    	
+  	</tests>
+
 <help>
 	Convert mascot results from mascotdat to pepXML
 </help>
diff -r d9564913a944 -r 327b2d99d4c5 repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Mar 05 00:18:41 2013 -0500
+++ b/repository_dependencies.xml	Sun Jun 09 08:17:38 2013 -0500
@@ -1,10 +1,6 @@
 <?xml version="1.0"?>
-<repositories description="Proteomics datatypes and mascot2xml from the TPP">
-
-     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="463328a6967f"/>
+<repositories description="Requires the Proteomics Datatypes package">
 
-	<repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/>
+     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="09b89b345de2"/>
 
-     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349"/>
-
- </repositories>
+</repositories>
diff -r d9564913a944 -r 327b2d99d4c5 tool-data/mascot_databases.loc.sample
--- a/tool-data/mascot_databases.loc.sample	Tue Mar 05 00:18:41 2013 -0500
+++ b/tool-data/mascot_databases.loc.sample	Sun Jun 09 08:17:38 2013 -0500
@@ -9,5 +9,5 @@
 # Entries should follow the be structured as follows
 # Display_name dbkey dbNameOnMascot dbkey
 #
-Swissprot	spall_	SPAll	spall_
+Swissprot	spall_	SwissProt	spall_
 Swissprot Human	sphuman_	SPHuman	sphuman_
\ No newline at end of file
diff -r d9564913a944 -r 327b2d99d4c5 tool-data/pepxml_databases.loc.sample
--- a/tool-data/pepxml_databases.loc.sample	Tue Mar 05 00:18:41 2013 -0500
+++ b/tool-data/pepxml_databases.loc.sample	Sun Jun 09 08:17:38 2013 -0500
@@ -6,7 +6,7 @@
 # Display_name omssa_tandem_dbname dbkey
 #
 #
-Swissprot	spall_	spall	spall_
+Swissprot	spall_	SwissProt	spall_
 Combined PlasmboDB (falciparum) and Swissprot Human	plasmodb_pfalciparum_sphuman_	plasmodb_pfalciparum_sphuman	plasmodb_pfalciparum_sphuman_
 Swissprot Human	sphuman_	sphuman	sphuman_
 Combined Swissprot/TRembl Human	sptrhuman_	sptrhuman	sptrhuman_
diff -r d9564913a944 -r 327b2d99d4c5 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Mar 05 00:18:41 2013 -0500
+++ b/tool_dependencies.xml	Sun Jun 09 08:17:38 2013 -0500
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
 
-    <package name="galaxy_protk" version="1.2.0">
-	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/>
+    <package name="galaxy_protk" version="1.2.2">
+	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/>
     </package>
 
 	<package name="trans_proteomic_pipeline" version="4.6.1">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349" />
+        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="e85a18371516"/>
     </package>
 
-</tool_dependency>
\ No newline at end of file
+</tool_dependency>